CXC chemokine receptor 4 (CXCR4)/CXC motif ligand 12 (CXCL12) and E-(endothelial)-selectin/E-selectin ligands (E-selectin-L) axes play critical roles in leukemia cell homing to the bone marrow niche and are closely associated with resistance to FLT3-targeted therapy in FLT3-mutant acute myeloid leukemia (AML) patients. Hence, it is imperative to co-target CXCR4/E-selectin/FLT3 in FLT3 mutant AML. Herein, we determined whether FLT3 inhibition modulates CXCR4/E-selectin-L levels and whether co-targeting CXCR4/E-selectin enhances the anti-leukemia effects and reduces bone marrow niche-mediated resistance in FLT3-targeted therapy. Our results demonstrate that CXCR4/E-selectin-L are transcriptionally upregulated by FLT3 inhibition. Concomitant blockage of CXCR4/E-selectin with the dual inhibitor GMI-1359 disrupts leukemia cell homing and migration to bone marrow niches. Combination treatment with GMI-1359 and quizartinib significantly reduced leukemia cell burden and extended mouse survival in a patient derived xenograft AML mouse model. These findings provide pre-clinical rationale for combined CXCR4/E-selectin/FLT3 targeting in FLT3-mutant AML.